Extending the Range of Rupture Force Measurements with Axial Optical Tweezers,
Z. Zhang and J. N. Milstein (preprint @ bioRxiv, 2023 ).

INSPIRE: Development of an Interdisciplinary Science Program in Research and Entrepreneurship,
T. Sedighi, T. Radu, Q. Ashraf, B. Kumar, E. Quilates, R. Rahmatullah, and J. N. Milstein (preprint @ chemRxiv, 2023 ).

Spatial exclusion leads to tug-of-war ecological dynamics between competing species within microchannels,
J. Rothschild, T. Ma, J. N. Milstein and A. Zilman (preprint @ bioRxiv, 2023 ).

Single-Molecule Counting Applied to the Study of GPCR Oligomerization,
J. N. Milstein, D. F. Nino, X. Zhou and C. Gradinaru , Biophys. J. 121, 3175-3187 (2022).

An Expectation-Maximization Approach to Quantifying Protein Stoichiometry with Single-Molecule Imaging,
A. Boonkird, D. F. Nino and J. N. Milstein, Bioinformatics Advances 1, vbab032 (2021).

Highly Potent Photoinactivation of Bacteria Using a Water-Soluble, Cell-Permeable, DNA-Binding Photosensitizer,
E. M. Digby, T. Ma, W. R. Zipfel, J. N. Milstein and A. A. Beharry, ACS Infectious Diseases 7, 3052–3061 (2021).

Estimating the Dynamic Range of Quantitative Single-Molecule Localization Microscopy,
D. Nino and J. N. Milstein, Biophys. J. 120, 3901-3910 (2021).

An Ultra-Stable and Dense Single-Molecule Click Platform for Sensing Protein-Deoxyribonucleic Acid Interactions,
E. Visser, J. Miladinovic and J. N. Milstein, Small Methods 5, 2001180, (2021).

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy,
D. Nino, D. Djayakarsana and J. N. Milstein, PLoS Computational Biology 16(12): e1008479 (2020).

Sensitive Detection of Broad-Spectrum Bacteria with Small-Molecule Fluorescent Excimer Chemosensors ,
A. Cabral, N. Rafiei, E. de Araujo, T. Radu, K. Toutah, D. Nino, J. N. Milstein, D. Kraskouskaya and P. Gunning, ACS Sensors 5, 2753−2762 (2020).

Extending the Photobleaching Lifetime in the Presence of an Optical Trap by Wavefront Engineering,
Z. Zhang and J. N. Milstein, Journal of Optics 22, 095301 (2020).

Growth Phase Dependent Chromosome Condensation and H-NS Protein Redistribution in E. coli Under Osmotic Stress,
N. Rafiei, M. Cordova, W. W. Navarre and J. N. Milstein, Journal of Bacteriology 23, e00469-19 (2019).

Nanoscopic Stoichiometry and Single-Molecule Counting,
D. Nino, D. Djayakarsana and J. N. Milstein, Small Methods 3, 1900082, (2019).

Fabrication and Characterization of a Microfluidic Flow Cytometer for the Advanced Undergraduate Laboratory,
D. Gorelik, F. Alam, J. N. Milstein and P. Piunno, Am. J. Phys. 87, 214-222 (2019).

Accounting for polarization in the calibration of a donut beam axial optical tweezers,
R. Pollari and J. N. Milstein, PLoS ONE 13(2): e0193402 (2018).

Resolving biology beyond the diffraction limit with single-molecule localization microscopy,
N. Rafiei, D. Nino and J. N. Milstein, Physics in Canada 73, 82-86 (2017).

Molecular Counting with Localization Microscopy: A Bayesian estimate based on fluorophore statistics,
D. Nino, N. Rafiei, Y. Wang, A. Zilman and J. N. Milstein, Biophys. J. 112, 1777-1785 (2017).

Xenogeneic silencing and its impact on bacterial genomes,
K. Singh, J. N. Milstein and W. W. Navarre, Annu. Rev. Microbiol. 70, 199-213 (2016).

Quantitative localization microscopy reveals a novel organization of a high-copy number plasmid,
Y. Wang, P. Penkul and J. N. Milstein, Biophys. J. 111, 467-479 (2016).

Fast Optimized Cluster Algorithm for Localizations (FOCAL): A spatial cluster analysis optimized for super-resolved microscopy,
A. Mazouchi and J. N. Milstein, Bioinformatics 32(5), 747–754 (2016).

Simulation assisted analysis of the intrinsic stiffness for short DNA molecules imaged with scanning atomic force microscopy,
H. Wang and J. N. Milstein, PLoS ONE 10(11), e0142277 (2015).

Improved axial trapping with holographic optical tweezers,
R. Pollari and J. N. Milstein, Opt. Express 23, 28857-28867 (2015).

Axial optical traps: A new direction for optical tweezers,
S. Yehoshua, R. Pollari and J. N. Milstein, Biophys. J. 108, 2759-2766 (2015).

A biomechanical mechanism for initiating DNA packaging ,
H. Wang, S. Yehoshua, S. S. Ali, W. W. Navarre, and J. N. Milstein, Nucl. Acids Res. 42, 11921 (2014).

Rapid feedback control and stabilization of an optical tweezers with a budget microcontroller,
D. Nino, H. Wang and J. N. Milstein, Eur. J. Phys. 35, 055009 (2014).

Assorted Biophysics Papers (the postdoc years):

Two-color DNA nanoprobe of intracellular dynamics,
J. N. Milstein, M. Chu, K. Raghunathan, and J. -C. Meiners, Nano Lett. 12, 2515 (2012).

The worm-like chain (WLC) model,
J. N. Milstein and J. -C. Meiners, Encyclopedia of Biophysics, Springer-Verlag (2012).

Stretching short sequences of DNA with constant force axial optical tweezers,
K. Raghunathan, J. N. Milstein and J. -C. Meiners, J. Vis. Exp. 56, e3405 (2011).

On the role of DNA biomechanics in the regulation of gene expression,
J. N. Milstein and J. -C. Meiners J. R. Soc. Interface 8, 1673 (2011).

Bead-size effects on protein-mediated DNA looping in tethered particle motion experiments,
J. N. Milstein, Y. F. Chen and J. -C. Meiners, Biopolymers 95, 144 (2010).

Protein-mediated DNA loop formation and breakdown in a fluctuating environment,
Y. F. Chen*, J. N. Milstein* and J. -C. Meiners, Phys. Rev. Lett. 104, 258103 (2010).

Femtonewton entropic forces can control the formation of protein-mediated DNA loops,
Y. F. Chen, J. N. Milstein and J. -C. Meiners, Phys. Rev. Lett. 104, 048301 (2010).
(Designated as an Editors' Suggestion and spotlighted with an editorial Synopsis).

Neuronal shot noise and brownian 1/f^2 behavior in the local field potential,
J. N. Milstein, F. Mormann, I. Fried, and C. Koch, PLoS ONE 4(2), e4338 (2009).

Dynamic moment analysis of the extracellular electric field of a biologically realistic spiking neuron,
J. N. Milstein and C. Koch, Neural Comput. 20, 2070 (2008).
(Recommended by Faculty of 1000)

Cold Atom Papers from a Distant Life:

A study of classical field techniques for condensates in one-dimensional rings at finite temperatures,
A. Nunnenkamp, J. N. Milstein, and K. Burnett, Phys. Rev. A 75, 1 (2007).

Superfluidity and binary-correllations within clusters of fermions,
J. N. Milstein and K. Burnett, J. Phys. B 39, 1965 (2006).

From Cooper pairs to molecules: Effective field theories for ultra-cold atomic gases near Feshbach resonances,
Ph.D. Thesis, JILA, University of Colorado, Boulder (2004).

Resonant formation of strongly correlated paired states in rotating Bose gases,
S.G. Bhongale, J. N. Milstein and M. J. Holland, Phys. Rev. A 69, 053603 (2004).

The nature of superfluidity near a Feshbach resonance
Jelena Stajic, J. N. Milstein, Qijin Chen, M.J. Holland and K. Levin,
Phys. Rev. A 69, 063610 (2004).

Feshbach resonances and collapsing Bose-Einstein condensates,
*Quantum Gases Focus Issue*
J. N. Milstein, C. Menotti and M. Holland, N. J. Phys. 5, 52 (2003).

Resonance theory of the crossover from Bardeen-Cooper-Schrieffer superfluidity to Bose-Einstein condensation in a dilute Fermi gas,
J. N. Milstein, S. J. J. M. F. Kokkelmans and M. J. Holland,
Phys. Rev. A 66, 043604 (2002).

Resonance superfluidity: Renormalization of resonance scattering theory,
S. J. J. M. F. Kokkelmans, J. N. Milstein, M. L. Chiofalo, R. Walser and M. J. Holland,
Phys. Rev. A 65, 053617 (2002).
Signatures of resonance superfluidity in a quantum Fermi gas,
M. L. Chiofalo, S. J. J. M. F. Kokkelmans, J. N. Milstein and M. J. Holland,
Phys. Rev. Lett. 88, 090402 (2002).